Genes regulated in dendritic cell differentiation

Abstract

The present invention relates to a combination comprising a plurality of cDNAs which are differentially expressed in dendritic cells, which may be used in their entirety or in part to diagnose, to stage, to treat, or to monitor the treatment of a subject with cancer, infectious disease, autoimmunity, allergy, and graft versus host disease or to enhance a vaccine.

What is claimed is:  
     
         1 . A combination comprising a plurality of cDNAs that are differentially expressed in DC, and selected from SEQ ID NOs:1-260 or their complements.  
     
     
         2 . The combination of  claim 1 , wherein each of the cDNAs is downregulated in DC and is selected from SEQ ID NOs:1-29.  
     
     
         3 . The combination of  claim 1 , wherein each of the cDNAs is upregulated in DC and is selected from SEQ ID NOs:30-241.  
     
     
         4 . The combination of  claim 1 , wherein each of the cDNAs is upregulated in mature DC and is selected from SEQ ID NOs:242-257.  
     
     
         5 . The combination of  claim 1 , wherein each of the cDNAs is downregulated in mature DC and is selected from SEQ ID NOs:258-260.  
     
     
         6 . The combination of  claim 1 , wherein the cDNAs are immobilized on a substrate.  
     
     
         7 . A high throughput method for detecting differential expression of one or more cDNAs in a sample containing nucleic acids, the method comprising: 
 (a) hybridizing the substrate of  claim 6  with nucleic acids of the sample, thereby forming one or more hybridization complexes;    (b) detecting the hybridization complexes; and    (c) comparing the hybridization complexes with those of a standard, wherein differences between the standard and sample hybridization complexes indicate differential expression of cDNAs in the sample.    
     
     
         8 . The method of  claim 7 , wherein the nucleic acids of the sample are amplified prior to hybridization.  
     
     
         9 . The method of  claim 7 , wherein the sample is from a subject with cancer, infectious disease, autoimmunity, allergy, or graft versus host disease and comparison with a standard identifies or stages the disorder.  
     
     
         10 . A high throughput method of screening a plurality of molecules or compounds to identify a ligand which specifically binds a cDNA, the method comprising: 
 (a) combining the combination of  claim 1  with the plurality of molecules or compounds under conditions to allow specific binding; and    (b) detecting specific binding between each cDNA and at least one molecule or compound, thereby identifying a ligand that specifically binds to each cDNA.    
     
     
         11 . The method of  claim 10  wherein the plurality of molecules or compounds are selected from aptamers, DNA molecules, RNA molecules, peptide nucleic acid molecules, mimetics, peptides, transcription factors, repressors, and regulatory proteins.  
     
     
         12 . An isolated cDNA selected from the group consisting of SEQ ID NOs:24-29, 187-202, 205-213, 216-241, 256, 257, 259, and 260.  
     
     
         13 . A vector containing the cDNA of  claim 12 .  
     
     
         14 . A host cell containing the vector of  claim 13 .  
     
     
         15 . A method for producing a protein, the method comprising the steps of: 
 (a) culturing the host cell of  claim 14  under conditions for expression of protein; and    (b) recovering the protein from the host cell culture.    
     
     
         16 . A protein or a portion thereof produced by the method of  claim 15 .  
     
     
         17 . A high-throughput method for using a protein to screen a plurality of molecules or compounds to identify at least one ligand which specifically binds the protein, the method comprising: 
 (a) combining the protein of  claim 16  with the plurality of molecules or compounds under conditions to allow specific binding; and    (b) detecting specific binding between the protein and a molecule or compound, thereby identifying a ligand which specifically binds the protein.    
     
     
         18 . The method of  claim 17  wherein the plurality of molecules or compounds is selected from DNA molecules, RNA molecules, peptide nucleic acid molecules, mimetics, peptides, proteins, agonists, antagonists, antibodies or their fragments, immunoglobulins, inhibitors, drug compounds, and pharmaceutical agents.  
     
     
         19 . A method of using a protein to produce an antibody, the method comprising: 
 a) immunizing an animal with the protein of  claim 16  under conditions to elicit an antibody response;    b) isolating animal antibodies; and    c) screening the isolated antibodies with the protein, thereby identifying an antibody which specifically binds the protein.    
     
     
         20 . A antibody produced by the method of  claim 19.